A citation-based method for searching scientific literature

Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
Times Cited: 821







List of co-cited articles
501 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


A gene expression map of the Arabidopsis root.
Kenneth Birnbaum, Dennis E Shasha, Jean Y Wang, Jee W Jung, Georgina M Lambert, David W Galbraith, Philip N Benfey. Science 2003
839
4

Single-cell transcriptional diversity is a hallmark of developmental potential.
Gunsagar S Gulati, Shaheen S Sikandar, Daniel J Wesche, Anoop Manjunath, Anjan Bharadwaj, Mark J Berger, Francisco Ilagan, Angera H Kuo, Robert W Hsieh, Shang Cai,[...]. Science 2020
58
6

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root.
Tian-Qi Zhang, Zhou-Geng Xu, Guan-Dong Shang, Jia-Wei Wang. Mol Plant 2019
82
4

Human haematopoietic stem cell lineage commitment is a continuous process.
Lars Velten, Simon F Haas, Simon Raffel, Sandra Blaszkiewicz, Saiful Islam, Bianca P Hennig, Christoph Hirche, Christoph Lutz, Eike C Buss, Daniel Nowak,[...]. Nat Cell Biol 2017
327
4

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma.
Hanjie Li, Anne M van der Leun, Ido Yofe, Yaniv Lubling, Dikla Gelbard-Solodkin, Alexander C J van Akkooi, Marlous van den Braber, Elisa A Rozeman, John B A G Haanen, Christian U Blank,[...]. Cell 2019
258
4

Single-cell RNA counting at allele and isoform resolution using Smart-seq3.
Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J M Larsson, Omid R Faridani, Rickard Sandberg. Nat Biotechnol 2020
70
5

Single-cell reconstruction of the early maternal-fetal interface in humans.
Roser Vento-Tormo, Mirjana Efremova, Rachel A Botting, Margherita Y Turco, Miquel Vento-Tormo, Kerstin B Meyer, Jong-Eun Park, Emily Stephenson, Krzysztof Polański, Angela Goncalves,[...]. Nature 2018
513
4

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Jiarui Ding, Xian Adiconis, Sean K Simmons, Monika S Kowalczyk, Cynthia C Hession, Nemanja D Marjanovic, Travis K Hughes, Marc H Wadsworth, Tyler Burks, Lan T Nguyen,[...]. Nat Biotechnol 2020
123
4

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
4

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
4

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Moshe Sade-Feldman, Keren Yizhak, Stacey L Bjorgaard, John P Ray, Carl G de Boer, Russell W Jenkins, David J Lieb, Jonathan H Chen, Dennie T Frederick, Michal Barzily-Rokni,[...]. Cell 2018
448
4

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
227
4

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.
Sofie Van Gassen, Britt Callebaut, Mary J Van Helden, Bart N Lambrecht, Piet Demeester, Tom Dhaene, Yvan Saeys. Cytometry A 2015
446
4

Generalizing RNA velocity to transient cell states through dynamical modeling.
Volker Bergen, Marius Lange, Stefan Peidli, F Alexander Wolf, Fabian J Theis. Nat Biotechnol 2020
171
4

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.
Sean C Bendall, Erin F Simonds, Peng Qiu, El-ad D Amir, Peter O Krutzik, Rachel Finck, Robert V Bruggner, Rachel Melamed, Angelica Trejo, Olga I Ornatsky,[...]. Science 2011
4

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
215
3

A systematic performance evaluation of clustering methods for single-cell RNA-seq data.
Angelo Duò, Mark D Robinson, Charlotte Soneson. F1000Res 2018
83
3

A Single-Cell Transcriptome Atlas of the Human Pancreas.
Mauro J Muraro, Gitanjali Dharmadhikari, Dominic Grün, Nathalie Groen, Tim Dielen, Erik Jansen, Leon van Gurp, Marten A Engelse, Francoise Carlotti, Eelco J P de Koning,[...]. Cell Syst 2016
373
3

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation.
Sonia Nestorowa, Fiona K Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola K Wilson, David G Kent, Berthold Göttgens. Blood 2016
237
3

Blood monocytes consist of two principal subsets with distinct migratory properties.
Frederic Geissmann, Steffen Jung, Dan R Littman. Immunity 2003
3

Single-Cell Multiomics: Multiple Measurements from Single Cells.
Iain C Macaulay, Chris P Ponting, Thierry Voet. Trends Genet 2017
217
3

Cerebral organoids model human brain development and microcephaly.
Madeline A Lancaster, Magdalena Renner, Carol-Anne Martin, Daniel Wenzel, Louise S Bicknell, Matthew E Hurles, Tessa Homfray, Josef M Penninger, Andrew P Jackson, Juergen A Knoblich. Nature 2013
3


Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.
Alex A Pollen, Aparna Bhaduri, Madeline G Andrews, Tomasz J Nowakowski, Olivia S Meyerson, Mohammed A Mostajo-Radji, Elizabeth Di Lullo, Beatriz Alvarado, Melanie Bedolli, Max L Dougherty,[...]. Cell 2019
150
3

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.
Suijuan Zhong, Shu Zhang, Xiaoying Fan, Qian Wu, Liying Yan, Ji Dong, Haofeng Zhang, Long Li, Le Sun, Na Pan,[...]. Nature 2018
217
3

Transcriptome and epigenome landscape of human cortical development modeled in organoids.
Anahita Amiri, Gianfilippo Coppola, Soraya Scuderi, Feinan Wu, Tanmoy Roychowdhury, Fuchen Liu, Sirisha Pochareddy, Yurae Shin, Alexias Safi, Lingyun Song,[...]. Science 2018
108
3

hESC-Derived Thalamic Organoids Form Reciprocal Projections When Fused with Cortical Organoids.
Yangfei Xiang, Yoshiaki Tanaka, Bilal Cakir, Benjamin Patterson, Kun-Yong Kim, Pingnan Sun, Young-Jin Kang, Mei Zhong, Xinran Liu, Prabir Patra,[...]. Cell Stem Cell 2019
107
3

Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex.
Taisuke Kadoshima, Hideya Sakaguchi, Tokushige Nakano, Mika Soen, Satoshi Ando, Mototsugu Eiraku, Yoshiki Sasai. Proc Natl Acad Sci U S A 2013
423
3

Fusion of Regionally Specified hPSC-Derived Organoids Models Human Brain Development and Interneuron Migration.
Yangfei Xiang, Yoshiaki Tanaka, Benjamin Patterson, Young-Jin Kang, Gubbi Govindaiah, Naomi Roselaar, Bilal Cakir, Kun-Yong Kim, Adam P Lombroso, Sung-Min Hwang,[...]. Cell Stem Cell 2017
227
3

Cell diversity and network dynamics in photosensitive human brain organoids.
Giorgia Quadrato, Tuan Nguyen, Evan Z Macosko, John L Sherwood, Sung Min Yang, Daniel R Berger, Natalie Maria, Jorg Scholvin, Melissa Goldman, Justin P Kinney,[...]. Nature 2017
451
3

Cell stress in cortical organoids impairs molecular subtype specification.
Aparna Bhaduri, Madeline G Andrews, Walter Mancia Leon, Diane Jung, David Shin, Denise Allen, Dana Jung, Galina Schmunk, Maximilian Haeussler, Jahan Salma,[...]. Nature 2020
116
3

Cerebral organoids at the air-liquid interface generate diverse nerve tracts with functional output.
Stefano L Giandomenico, Susanna B Mierau, George M Gibbons, Lea M D Wenger, Laura Masullo, Timothy Sit, Magdalena Sutcliffe, Jerome Boulanger, Marco Tripodi, Emmanuel Derivery,[...]. Nat Neurosci 2019
139
3

Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure.
Xuyu Qian, Ha Nam Nguyen, Mingxi M Song, Christopher Hadiono, Sarah C Ogden, Christy Hammack, Bing Yao, Gregory R Hamersky, Fadi Jacob, Chun Zhong,[...]. Cell 2016
916
3


Multiplexed quantification of proteins and transcripts in single cells.
Vanessa M Peterson, Kelvin Xi Zhang, Namit Kumar, Jerelyn Wong, Lixia Li, Douglas C Wilson, Renee Moore, Terrill K McClanahan, Svetlana Sadekova, Joel A Klappenbach. Nat Biotechnol 2017
293
3

Highly scalable generation of DNA methylation profiles in single cells.
Ryan M Mulqueen, Dmitry Pokholok, Steven J Norberg, Kristof A Torkenczy, Andrew J Fields, Duanchen Sun, John R Sinnamon, Jay Shendure, Cole Trapnell, Brian J O'Roak,[...]. Nat Biotechnol 2018
78
3

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome.
Chenxu Zhu, Miao Yu, Hui Huang, Ivan Juric, Armen Abnousi, Rong Hu, Jacinta Lucero, M Margarita Behrens, Ming Hu, Bing Ren. Nat Struct Mol Biol 2019
53
5

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.
Hannah A Pliner, Jonathan S Packer, José L McFaline-Figueroa, Darren A Cusanovich, Riza M Daza, Delasa Aghamirzaie, Sanjay Srivatsan, Xiaojie Qiu, Dana Jackson, Anna Minkina,[...]. Mol Cell 2018
134
3

Somatic mutations and cell identity linked by Genotyping of Transcriptomes.
Anna S Nam, Kyu-Tae Kim, Ronan Chaligne, Franco Izzo, Chelston Ang, Justin Taylor, Robert M Myers, Ghaith Abu-Zeinah, Ryan Brand, Nathaniel D Omans,[...]. Nature 2019
69
4

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
3

Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin Lymphoma.
Tomohiro Aoki, Lauren C Chong, Katsuyoshi Takata, Katy Milne, Monirath Hav, Anthony Colombo, Elizabeth A Chavez, Michael Nissen, Xuehai Wang, Tomoko Miyata-Takata,[...]. Cancer Discov 2020
48
6

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging.
Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry P Nolan. Cell 2018
266
3

Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
543
3

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Florian Buettner, Kedar N Natarajan, F Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J Theis, Sarah A Teichmann, John C Marioni, Oliver Stegle. Nat Biotechnol 2015
561
3

Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data.
George C Linderman, Manas Rachh, Jeremy G Hoskins, Stefan Steinerberger, Yuval Kluger. Nat Methods 2019
82
3

SCnorm: robust normalization of single-cell RNA-seq data.
Rhonda Bacher, Li-Fang Chu, Ning Leng, Audrey P Gasch, James A Thomson, Ron M Stewart, Michael Newton, Christina Kendziorski. Nat Methods 2017
125
3

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
3


SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization.
Shintaro Katayama, Virpi Töhönen, Sten Linnarsson, Juha Kere. Bioinformatics 2013
66
4



Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.